Rapid Determination of RNA Modifications in Consensus Motifs by Nuclease Protection with Ion-Tagged Oligonucleotide Probes and Matrix-Assisted Laser Desorption Ionization Mass Spectrometry

scDART-seq reveals distinct m6A signatures and mRNA methylation heterogeneity in single cells

(2022) Matthew Tegowski et al.   MOLECULAR CELL

Pseudouridine synthase 7 is an opportunistic enzyme that binds and modifies substrates with diverse sequences and structures

(2022) Meredith K. Purchal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

m6A RNA modifications are measured at single-base resolution across the mammalian transcriptome

(2022) Lulu Hu et al.   NATURE BIOTECHNOLOGY

Cell culture NAIL-MS allows insight into human tRNA and rRNA modification dynamics in vivo

(2021) Matthias Heiss et al.   Nature Communications

RNA Metabolism Guided by RNA Modifications: The Role of SMUG1 in rRNA Quality Control

(2021) Lisa Lirussi et al.   Biomolecules

Characterization of Neuronal RNA Modifications during Non-associative Learning in Aplysia Reveals Key Roles for tRNAs in Behavioral Sensitization

(2021) Kevin D. Clark et al.   ACS Central Science

Single-Neuron RNA Modification Analysis by Mass Spectrometry: Characterizing RNA Modification Patterns and Dynamics with Single-Cell Resolution

(2021) Kevin D. Clark et al.   ANALYTICAL CHEMISTRY

METTL3-dependent RNA m6A dysregulation contributes to neurodegeneration in Alzheimer’s disease through aberrant cell cycle events

(2021) Fanpeng Zhao et al.   Molecular Neurodegeneration

MODOMICS: a database of RNA modification pathways. 2021 update

(2021) Pietro Boccaletto et al.   NUCLEIC ACIDS RESEARCH

Broadly applicable oligonucleotide mass spectrometry for the analysis of RNA writers and erasers in vitro

(2020) Felix Hagelskamp et al.   NUCLEIC ACIDS RESEARCH

Biphasic Liquid Microjunction Extraction for Profiling Neuronal RNA Modifications by Liquid Chromatography–Tandem Mass Spectrometry

(2020) Kevin David Clark et al.   ANALYTICAL CHEMISTRY

NOseq: amplicon sequencing evaluation method for RNA m6A sites after chemical deamination

(2020) Stephan Werner et al.   NUCLEIC ACIDS RESEARCH

Oligonucleotide analysis by hydrophilic interaction liquid chromatography-mass spectrometry in the absence of ion-pair reagents

(2019) Peter A. Lobue et al.   JOURNAL OF CHROMATOGRAPHY A

Maximizing Ion-Tagged Oligonucleotide Loading on Magnetic Ionic Liquid Supports for the Sequence-Specific Extraction of Nucleic Acids

(2019) Kevin D. Clark et al.   ANALYTICAL CHEMISTRY

Transcriptome-wide Mapping of Internal N7-Methylguanosine Methylome in Mammalian mRNA

(2019) Li-Sheng Zhang et al.   MOLECULAR CELL

Where, When, and How: Context-Dependent Functions of RNA Methylation Writers, Readers, and Erasers

(2019) Hailing Shi et al.   MOLECULAR CELL

The dynamics of FTO binding and demethylation from the m6A motifs

(2019) Yixing Li et al.   RNA Biology

Sequence-specific preconcentration of a mutation prone KRAS fragment from plasma using ion-tagged oligonucleotides coupled to qPCR compatible magnetic ionic liquid solvents

(2019) Miranda N. Emaus et al.   ANALYTICA CHIMICA ACTA

Arabidopsis thaliana ITS sequence-specific DNA extraction by ion-tagged oligonucleotides coupled with a magnetic ionic liquid

(2019) Arianna Marengo et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

A general LC-MS-based RNA sequencing method for direct analysis of multiple-base modifications in RNA mixtures

(2019) Ning Zhang et al.   NUCLEIC ACIDS RESEARCH

Selective hybridization and capture of KRAS DNA from plasma and blood using ion-tagged oligonucleotide probes coupled to magnetic ionic liquids

(2019) Miranda N. Emaus et al.   ANALYTICA CHIMICA ACTA

Dynamic transcriptomic m6A decoration: writers, erasers, readers and functions in RNA metabolism

(2018) Ying Yang et al.   CELL RESEARCH

Epitranscriptomic m 6 A Regulation of Axon Regeneration in the Adult Mammalian Nervous System

(2018) Yi-Lan Weng et al.   NEURON

m6A mRNA methylation regulates AKT activity to promote the proliferation and tumorigenicity of endometrial cancer

(2018) Jun Liu et al.   NATURE CELL BIOLOGY

METTL3-mediated N6-methyladenosine mRNA modification enhances long-term memory consolidation

(2018) Zeyu Zhang et al.   CELL RESEARCH

Sequencing-based methods for detection and quantitation of ribose methylations in RNA

(2018) Nicolai Krogh et al.   METHODS

Cap-specific terminal N6-methylation of RNA by an RNA polymerase II–associated methyltransferase

(2018) Shinichiro Akichika et al.   SCIENCE

Base-Resolution Mapping Reveals Distinct m 1 A Methylome in Nuclear- and Mitochondrial-Encoded Transcripts

(2017) Xiaoyu Li et al.   MOLECULAR CELL

Detecting RNA modifications in the epitranscriptome: predict and validate

(2017) Mark Helm et al.   NATURE REVIEWS GENETICS

Determination of DNA and RNA Methylation in Circulating Tumor Cells by Mass Spectrometry

(2016) Wei Huang et al.   ANALYTICAL CHEMISTRY

Experience-Dependent Accumulation of N 6 -Methyladenosine in the Prefrontal Cortex Is Associated with Memory Processes in Mice

(2016) Jocelyn Widagdo et al.   JOURNAL OF NEUROSCIENCE

Reversible methylation of m6Am in the 5′ cap controls mRNA stability

(2016) Jan Mauer et al.   NATURE

Transcriptome-wide distribution and function of RNA hydroxymethylcytosine

(2016) B. Delatte et al.   SCIENCE

Going global: the new era of mapping modifications in RNA

(2016) Patrick A. Limbach et al.   Wiley Interdisciplinary Reviews-RNA

Cy3 and Cy5 dyes attached to oligonucleotide terminus stabilize DNA duplexes: Predictive thermodynamic model

(2015) Bernardo G. Moreira et al.   BIOPHYSICAL CHEMISTRY

Structure and Thermodynamics of N6-Methyladenosine in RNA: A Spring-Loaded Base Modification

(2015) Caroline Roost et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Dynamic m6A mRNA methylation directs translational control of heat shock response

(2015) Jun Zhou et al.   NATURE

Gene expression regulation mediated through reversible m6A RNA methylation

(2014) Ye Fu et al.   NATURE REVIEWS GENETICS

A METTL3–METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation

(2013) Jianzhao Liu et al.   Nature Chemical Biology

The fat mass and obesity associated gene (Fto) regulates activity of the dopaminergic midbrain circuitry

(2013) Martin E Hess et al.   NATURE NEUROSCIENCE

Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons

(2012) Kate D. Meyer et al.   CELL

Yeast Rrp8p, a novel methyltransferase responsible for m1A 645 base modification of 25S rRNA

(2012) Christian Peifer et al.   NUCLEIC ACIDS RESEARCH

N6-Methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO

(2011) Guifang Jia et al.   Nature Chemical Biology

A Quantitative Systems Approach Reveals Dynamic Control of tRNA Modifications during Cellular Stress

(2010) Clement T. Y. Chan et al.   PLoS Genetics

Ariadne: a database search engine for identification and chemical analysis of RNA using tandem mass spectrometry data

(2009) Hiroshi Nakayama et al.   NUCLEIC ACIDS RESEARCH